套件： qiime (1.8.0+dfsg-4ubuntu1)

qiime 的相關超連結

Trisquel 的資源：

下載原始碼套件 qiime：

維護者：

Ubuntu Developers (郵件存檔)

Original Maintainers:

Debian Med Packaging Team (郵件存檔)
Steffen Moeller
Tim Booth
Andreas Tille

外部的資源：

主頁 [www.qiime.org]

相似套件：

Quantitative Insights Into Microbial Ecology

QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. A standard QIIME analysis begins with sequence data from one or more sequencing platforms, including

 * Sanger,
 * Roche/454, and
 * Illumina GAIIx.

With all the underlying tools installed, of which not all are yet available in Debian (or any other Linux distribution), QIIME can perform

 * library de-multiplexing and quality filtering;
 * denoising with PyroNoise;
 * OTU and representative set picking with uclust, cdhit, mothur, BLAST,
   or other tools;
 * taxonomy assignment with BLAST or the RDP classifier;
 * sequence alignment with PyNAST, muscle, infernal, or other tools;
 * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
 * alpha diversity and rarefaction, including visualization of results,
   using over 20 metrics including Phylogenetic Diversity, chao1, and
   observed species;
 * beta diversity and rarefaction, including visualization of results,
   using over 25 metrics including weighted and unweighted UniFrac,
   Euclidean distance, and Bray-Curtis;
 * summarization and visualization of taxonomic composition of samples
   using pie charts and histograms

and many other features.

QIIME includes parallelization capabilities for many of the computationally intensive steps. By default, these are configured to utilize a mutli-core environment, and are easily configured to run in a cluster environment. QIIME is built in Python using the open-source PyCogent toolkit. It makes extensive use of unit tests, and is highly modular to facilitate custom analyses.

其他與 qiime 有關的套件

依賴

推薦

建議

dep: fasttree

phylogenetic trees from alignments of nucleotide or protein sequences
dep: king

interactive system for three-dimensional vector graphics
dep: libc6 (>= 2.15)

GNU C Library: Shared libraries
同時作為一個虛擬套件由這些套件提供： libc6-udeb
dep: libffi6 (>= 3.0.4)

Foreign Function Interface library runtime
dep: libgmp10

Multiprecision arithmetic library
dep: libjs-jquery

JavaScript library for dynamic web applications
dep: pynast (>= 1.2.2)

alignment of short DNA sequences
dep: python (<< 2.8)

interactive high-level object-oriented language (default version)

dep: python (>= 2.7)
dep: python-biom-format (>= 1.2.0)

Biological Observation Matrix (BIOM) format (Python 2)
dep: python-cogent (>= 1.5.3)

framework for genomic biology
dep: python-matplotlib

Python based plotting system in a style similar to Matlab
dep: python-numpy

Numerical Python adds a fast array facility to the Python language
dep: python-qcli

separated module of pyqi needed for QIIME package

rec: ampliconnoise

removal of noise from 454 sequenced PCR amplicons
rec: blast2

transitional dummy package to ncbi-blast+-legacy

或者 blast+-legacy

套件暫時不可用
rec: cd-hit

suite of programs designed to quickly group sequences
rec: chimeraslayer

detects likely chimeras in PCR amplified DNA
rec: clearcut

extremely efficient phylogenetic tree reconstruction
rec: infernal

inference of RNA secondary structural alignments
rec: muscle

Multiple alignment program of protein sequences
rec: parsinsert

Parsimonious Insertion of unclassified sequences into phylogenetic trees
rec: python-mpi4py

bindings of the Message Passing Interface (MPI) standard
rec: qiime-data

Quantitative Insights Into Microbial Ecology (supporting data)
rec: r-cran-optparse

GNU/R Command line option parser

sug: cytoscape

套件暫時不可用
sug: emperor

套件暫時不可用
sug: rdp-classifier

extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
sug: t-coffee

Multiple Sequence Alignment
sug: torque-client

套件暫時不可用

下載 qiime

下載可用於所有硬體架構的
硬體架構	套件大小	安裝後大小	檔案
amd64	914.1 kB	5364 kB	[文件列表]

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